- *Paleontological and Geochronological Investigations of the Eocene Oligocene Transition in Northeastern Washington State, Pacific Northwest* (M.S. Thesis, Western Washington University, 2001).
- *New Perspectives on the Origins and Early Evolutionary History of Birds: a Comprehensive Review Of Evidence from Fossils, Molecules and Developmental Biology* (Ph.D. Thesis, University of Southern California, 2006).
- *The Enigmatic Fossil Taxa Sinocalliopteryx gigas Xu et al 1999 and Caudipteryx zoui qiang et al 1998 and Their Relationship To Modern Aves* (2006)
Articles
- Szalay, F. S. (2004). New perspectives on the origin of birds. Palaeontologia Electronica, 7(2), 1-32.
- Szalay, F. S., Sargis, E. J., & Stafford Jr, B. J. (2005). Phylogenetic relationships of paleocene mammals to primates. Journal of Human Evolution, 48(1), 1-28.
- Szalay, F. S., & Sargis, E. J. (2006). The evolutionary history of lemurs and primates: a new understanding based on molecular and paleontological evidence. Evolutionary Anthropology, 15(2), 74-90.
- Szalay, F. S., Sargis, E. J., & Stafford Jr, B. J. (2007). Phylogenetic relationships of the anthropoid primates: a new interpretation based on molecular and paleontological evidence. Journal of Human Evolution, 53(1), 32-55.
- Szalay, F. S. (2009). The early evolution of birds: a phylogenetic analysis based on the fossil record. Journal of Vertebrate Paleontology, 29(1), 1-100.
- Szalay, F. S., Sargis, E. J., & Stafford Jr, B. J. (2010). Phylogenetic relationships of the lemurs and anthropoids: a new interpretation based on molecular and paleontological evidence. Journal of Human Evolution, 58(1), 1-22.
- Szalay, F. S., & Sargis, E. J. (2011). Primate origins: a new look based on molecular and paleontological evidence. Evolutionary Anthropology, 20(5), 189-200.
- Szalay, F. S., & Sargis, E. J. (2012). The evolutionary history of the primates. Annual Review of Anthropology, 41, 339-358.
- Szalay, F. S., Sargis, E. J., & Stafford Jr, B. J. (2013). Anthropoid relationships: a new interpretation based on molecular and paleontological evidence. Journal of Human Evolution, 64(5), 479-496.